MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2001/03/01 11:41:04)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE crp0.s (nucleotide)
Last updated on Thu Mar 1 08:28:36 2001
Database contains 18 sequences, 1890 residues
Scores for positive and reverse complement strands are combined.
MOTIFS meme.crp0.tcm.4.sunsparcsolaris.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 19 TGTGAGCGAGGTCACACTT
2 11 GTGGAATTGTT
3 8 CGGCGGGG
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.28
3 0.33 0.30
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.281 C 0.222 G 0.229 T 0.267
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 18 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
| Links | Sequence Name | Description | E-value | Length
|
|---|
|
| gale
|
| 0.00011
| 105
|
|
| lac
|
| 0.00041
| 105
|
|
| male
|
| 0.001
| 105
|
|
| tnaa
|
| 0.001
| 105
|
|
| malt
|
| 0.0019
| 105
|
|
| ara
|
| 0.0027
| 105
|
|
| ilv
|
| 0.004
| 105
|
|
| ce1cg
|
| 0.0098
| 105
|
|
| uxu1
|
| 0.023
| 105
|
|
| deop2
|
| 0.066
| 105
|
|
| ompa
|
| 0.084
| 105
|
|
| cya
|
| 0.086
| 105
|
|
| tdc
|
| 0.13
| 105
|
|
| bglr1
|
| 0.16
| 105
|
|
| crp
|
| 0.21
| 105
|
|
| malk
|
| 0.24
| 105
|
|
| pbr322
|
| 0.27
| 105
|
|
| trn9cat
|
| 9.4
| 105
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
A minus sign indicates that the occurrence is on the
reverse complement strand.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect |    Motifs
|
|---|
|
| gale
| 0.00011
|
|
|
| lac
| 0.00041
|
|
|
| male
| 0.001
|
|
|
| tnaa
| 0.001
|
|
|
| malt
| 0.0019
|
|
|
| ara
| 0.0027
|
|
|
| ilv
| 0.004
|
|
|
| ce1cg
| 0.0098
|
|
|
| uxu1
| 0.023
|
|
|
| deop2
| 0.066
|
|
|
| ompa
| 0.084
|
|
|
| cya
| 0.086
|
|
|
| tdc
| 0.13
|
|
|
| bglr1
| 0.16
|
|
|
| crp
| 0.21
|
|
|
| malk
| 0.24
|
|
|
| pbr322
| 0.27
|
|
|
| trn9cat
| 9.4
|
|
| SCALE
|
|
|---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence (a minus sign indicates that
the occurrence is on the reverse complement strand),
- the position p-value of the occurrence,
- the best possible match to the motif (or its reverse complement), and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
gale
LENGTH = 105 COMBINED P-VALUE = 6.33e-06 E-VALUE = 0.00011
DIAGRAM: 30-[-2]-3-[+1]-42
[-2] [+1]
1.8e-06 6.6e-07
AACAATTCCAC TGTGAGCGAGGTCACACTT
+++++++++++ +++ ++++++++++++++
1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTG
lac
LENGTH = 105 COMBINED P-VALUE = 2.26e-05 E-VALUE = 0.00041
DIAGRAM: 11-[+1]-46-[+2]-7-[-2]
[+1]
9.2e-06
TGTGAGCGAGGTCACACTT
++++++ ++ ++++ +++
1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG
[+2] [-2]
1.8e-06 6.6e-07
GTGGAATTGTT AACAATTCCAC
+++++++++++ +++++++++++
76 TGTGGAATTGTGAGCGGATAACAATTTCAC
male
LENGTH = 105 COMBINED P-VALUE = 5.60e-05 E-VALUE = 0.001
DIAGRAM: 16-[+1]-5-[+3]-57
[+1] [+3]
1.4e-06 1.5e-05
TGTGAGCGAGGTCACACTT CGGCGGGG
+++ + +++ ++++++++ ++++++++
1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGG
tnaa
LENGTH = 105 COMBINED P-VALUE = 5.68e-05 E-VALUE = 0.001
DIAGRAM: 73-[+1]-1-[-2]-1
[+
1.
TG
++
1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTG
1] [-2]
0e-05 2.4e-06
TGAGCGAGGTCACACTT AACAATTCCAC
++++ + +++++ ++ +++++++++++
76 TGATTCGATTCACATTTAAACAATTTCAGA
malt
LENGTH = 105 COMBINED P-VALUE = 1.08e-04 E-VALUE = 0.0019
DIAGRAM: 40-[-1]-46
[-1]
6.6e-07
AAGTGTGACCTCGCTCACA
++++++++++ + +++++
1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAA
ara
LENGTH = 105 COMBINED P-VALUE = 1.49e-04 E-VALUE = 0.0027
DIAGRAM: 57-[+1]-29
[+1]
2.4e-08
TGTGAGCGAGGTCACACT
+++++ ++ +++++++++
1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACT
T
+
76 TTGCTATGCCATAGCATTTTTATCCATAAG
ilv
LENGTH = 105 COMBINED P-VALUE = 2.23e-04 E-VALUE = 0.004
DIAGRAM: 4-[+3]-29-[+1]-45
[+3] [+1]
7.0e-06 1.9e-05
CGGCGGGG TGTGAGCGAGGTCACACTT
++++++++ +++++++ ++ + +++++
1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAA
ce1cg
LENGTH = 105 COMBINED P-VALUE = 5.44e-04 E-VALUE = 0.0098
DIAGRAM: 16-[-1]-28-[+1]-23
[-1] [+1]
5.2e-06 5.3e-07
AAGTGTGACCTCGCTCACA TGTGAGCGAGGT
+++++++ +++++ +++++ ++++++++ + +
1 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTT
CACACTT
+++++++
76 CACAAAAATGGAAGTCCACAGTCTTGACAG
uxu1
LENGTH = 105 COMBINED P-VALUE = 1.25e-03 E-VALUE = 0.023
DIAGRAM: 9-[+2]-85
[+2]
6.6e-07
GTGGAATTGTT
+++++++++++
1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAG
deop2
LENGTH = 105 COMBINED P-VALUE = 3.64e-03 E-VALUE = 0.066
DIAGRAM: 9-[+1]-31-[-1]-27
[+1] [-1]
1.9e-06 1.3e-06
TGTGAGCGAGGTCACACTT AAGTGTGACCTCGCTC
+++++ ++++ ++ ++ ++ ++++++++ +++ +++
1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATC
ACA
+++
76 GAAGTGTGTTGCGGAGTAGATGTTAGAATA
ompa
LENGTH = 105 COMBINED P-VALUE = 4.67e-03 E-VALUE = 0.084
DIAGRAM: 50-[+1]-36
[+1]
8.3e-07
TGTGAGCGAGGTCACACTT
+ +++ +++ ++++++++
1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGT
cya
LENGTH = 105 COMBINED P-VALUE = 4.75e-03 E-VALUE = 0.086
DIAGRAM: 49-[-1]-37
[-1]
8.5e-06
AAGTGTGACCTCGCTCACA
+ ++++ + ++ +++++++
1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGA
tdc
LENGTH = 105 COMBINED P-VALUE = 7.26e-03 E-VALUE = 0.13
DIAGRAM: 78-[+1]-8
[+1]
6.7e-06
TGTGAGCGAGGTCACACTT
++++ + + ++++ +++++
76 TAATTTGTGAGTGGTCGCACATATCCTGTT
bglr1
LENGTH = 105 COMBINED P-VALUE = 8.63e-03 E-VALUE = 0.16
DIAGRAM: 78-[+1]-8
[+1]
4.0e-06
TGTGAGCGAGGTCACACTT
+++++++ +++++ + ++
76 AACTGTGAGCATGGTCATATTTTTATCAAT
crp
LENGTH = 105 COMBINED P-VALUE = 1.14e-02 E-VALUE = 0.21
DIAGRAM: 65-[+1]-21
[+1]
2.5e-06
TGTGAGCGAG
+++ + +++
1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGAC
GTCACACTT
++++++ ++
76 GTCACATTACCGTGCAGTACAGTTGATAGC
malk
LENGTH = 105 COMBINED P-VALUE = 1.31e-02 E-VALUE = 0.24
DIAGRAM: 60-[-1]-26
[-1]
2.2e-05
AAGTGTGACCTCGCT
+++ ++++ ++ +++
1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT
CACA
+++
76 TGCAAAAATCGTGGCGATTTTATGTGCGCA
pbr322
LENGTH = 105 COMBINED P-VALUE = 1.52e-02 E-VALUE = 0.27
DIAGRAM: 52-[-1]-34
[-1]
6.7e-06
AAGTGTGACCTCGCTCACA
++++++ ++ ++++++
1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG
trn9cat
LENGTH = 105 COMBINED P-VALUE = 5.24e-01 E-VALUE = 9.4
DIAGRAM: 105
Debugging Information
CPU: nbcr2
Time 0.080000 secs.
mast meme.crp0.tcm.4.sunsparcsolaris.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information